GitHub - starostinak/qc

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
scripts		scripts
src		src
CMakeLists.txt		CMakeLists.txt
CMakeLists.txt.user		CMakeLists.txt.user
Makefile		Makefile
README		README
qc.cbp		qc.cbp

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To compile the project, do following commands:
mkdir build
cd build 
cmake ..
make

To launch:
cd build
./qc reads.fq deviation out.fa
python ../scripts/specify_contaminant.sh blast_db threads_num out.fa
python ../scripts/remove_contaminant.py reads.fq sample_ref.fa.ind contaminant.fa.ind threads_num